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- EMDB-21050: Cryo-EM structure of an active human histone pre-mRNA 3'-end proc... -

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Basic information

Entry
Database: EMDB / ID: EMD-21050
TitleCryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution
Map dataactive human histone pre-mRNA 3'-end processing machinery
Sample
  • Complex: The core of metazoan replication-dependent histone pre-mRNA 3'-end processing machinery
    • Protein or peptide: x 10 types
    • RNA: x 2 types
  • Ligand: x 1 types
Function / homology
Function and homology information


histone mRNA metabolic process / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA 3'-end processing by stem-loop binding and cleavage / 5'-3' RNA exonuclease activity / U2 snRNP binding / nuclear stress granule / regulation of chromatin organization / Processing of Intronless Pre-mRNAs / U7 snRNA binding / histone pre-mRNA DCP binding ...histone mRNA metabolic process / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA 3'-end processing by stem-loop binding and cleavage / 5'-3' RNA exonuclease activity / U2 snRNP binding / nuclear stress granule / regulation of chromatin organization / Processing of Intronless Pre-mRNAs / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / mRNA cleavage and polyadenylation specificity factor complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome / mRNA 3'-end processing / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / Transport of Mature mRNA Derived from an Intronless Transcript / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / telomerase holoenzyme complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / : / termination of RNA polymerase II transcription / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of G1/S transition of mitotic cell cycle / bicellular tight junction / U5 snRNP / Cajal body / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / negative regulation of protein binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / postsynapse / cytoskeleton / nuclear body / cell adhesion / ribonucleoprotein complex / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Symplekin/Pta1 ...Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U7 snRNA-associated Sm-like protein LSm11 / Symplekin / U7 snRNA-associated Sm-like protein LSm10 / Cleavage and polyadenylation specificity factor subunit 2 / Cleavage and polyadenylation specificity factor subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSun Y / Zhang Y / Walz T / Tong L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM029832 United States
CitationJournal: Science / Year: 2020
Title: Structure of an active human histone pre-mRNA 3'-end processing machinery.
Authors: Yadong Sun / Yixiao Zhang / Wei Shen Aik / Xiao-Cui Yang / William F Marzluff / Thomas Walz / Zbigniew Dominski / Liang Tong /
Abstract: The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with ...The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with the canonical cleavage and polyadenylation machinery. We reconstituted an active human histone pre-mRNA processing machinery using 13 recombinant proteins and two RNAs and determined its structure by cryo-electron microscopy. The overall structure is highly asymmetrical and resembles an amphora with one long handle. We captured the pre-mRNA in the active site of the endonuclease, the 73-kilodalton subunit of the cleavage and polyadenylation specificity factor, poised for cleavage. The endonuclease and the entire cleavage module undergo extensive rearrangements for activation, triggered through the recognition of the duplex between the authentic pre-mRNA and U7 small nuclear RNA (snRNA). Our study also has notable implications for understanding canonical and snRNA 3'-end processing.
History
DepositionDec 2, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseFeb 19, 2020-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0243
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0243
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v4x
  • Surface level: 0.0243
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21050.png

Downloads & links

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Map

FileDownload / File: emd_21050.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationactive human histone pre-mRNA 3'-end processing machinery
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0243 / Movie #1: 0.0243
Minimum - Maximum-0.106328204 - 0.15815918
Average (Standard dev.)-2.8146926e-06 (±0.003455687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 357.38 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z334334334
origin x/y/z0.0000.0000.000
length x/y/z357.380357.380357.380
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS334334334
D min/max/mean-0.1060.158-0.000

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Supplemental data

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Sample components

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Entire : The core of metazoan replication-dependent histone pre-mRNA 3'-en...

EntireName: The core of metazoan replication-dependent histone pre-mRNA 3'-end processing machinery
Components
  • Complex: The core of metazoan replication-dependent histone pre-mRNA 3'-end processing machinery
    • Protein or peptide: Small nuclear ribonucleoprotein Sm D3
    • Protein or peptide: Small nuclear ribonucleoprotein-associated proteins B and B'
    • Protein or peptide: Small nuclear ribonucleoprotein F
    • Protein or peptide: Small nuclear ribonucleoprotein E
    • Protein or peptide: Small nuclear ribonucleoprotein G
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm10
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm11
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 3
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 2
    • Protein or peptide: Symplekin
    • RNA: U7 snRNAU7 small nuclear RNA
    • RNA: modified H2a pre-mRNA
  • Ligand: ZINC ION

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Supramolecule #1: The core of metazoan replication-dependent histone pre-mRNA 3'-en...

SupramoleculeName: The core of metazoan replication-dependent histone pre-mRNA 3'-end processing machinery
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: Small nuclear ribonucleoprotein Sm D3

MacromoleculeName: Small nuclear ribonucleoprotein Sm D3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.111671 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ VYIRGSKIR FLILPDMLKN APMLKSMKNK NQGSGAGRGK AAILKAQVAA RGRGRGMGRG NIFQKRR

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Macromolecule #2: Small nuclear ribonucleoprotein-associated proteins B and B'

MacromoleculeName: Small nuclear ribonucleoprotein-associated proteins B and B'
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.911931 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTVGKSSKML QHIDYRMRCI LQDGRIFIGT FKAFDKHMNL ILCDCDEFRK IKPKNSKQAE REEKRVLGLV LLRGENLVSM TVEGPPPKD TGIARV

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Macromolecule #3: Small nuclear ribonucleoprotein F

MacromoleculeName: Small nuclear ribonucleoprotein F / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.734171 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY IDGALSGHLG EVLIRCNNVL YIRGVEEEEE DGEMRE

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Macromolecule #4: Small nuclear ribonucleoprotein E

MacromoleculeName: Small nuclear ribonucleoprotein E / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.817601 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAYRGQGQKV QKVMVQPINL IFRYLQNRSR IQVWLYEQVN MRIEGCIIGF DEYMNLVLDD AEEIHSKTKS RKQLGRIMLK GDNITLLQS VSN

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Macromolecule #5: Small nuclear ribonucleoprotein G

MacromoleculeName: Small nuclear ribonucleoprotein G / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.579236 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSKAHPPELK KFMDKKLSLK LNGGRHVQGI LRGFDPFMNL VIDECVEMAT SGQQNNIGMV VIRGNSIIML EALERVLEHH HHHH

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Macromolecule #6: U7 snRNA-associated Sm-like protein LSm10

MacromoleculeName: U7 snRNA-associated Sm-like protein LSm10 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.102057 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAVSHSVKER TISENSLIIL LQGLQGRVTT VDLRDESVAH GRIDNVDAFM NIRLAKVTYT DRWGHQVKLD DLFVTGRNVR YVHIPDDVN ITSTIEQQLQ IIHRVRNFGG KGQGRWEFPP KNCK

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Macromolecule #7: U7 snRNA-associated Sm-like protein LSm11

MacromoleculeName: U7 snRNA-associated Sm-like protein LSm11 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.609793 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHSGG SMEERERGAR SAGAGSPARP PSPRLDVSSD SFDPLLALYA PRLPPIPYPN APCFNNVAEY ESFLRTGVRG GGRGRGRAR GAAAGSGVPA APGPSGRTRR RPDAPAPDPE RIQRLRRLMV AKEEGDGAAG AGRRGPGRSR KAPRNVLTRM P LHEGSPLG ...String:
MHHHHHHSGG SMEERERGAR SAGAGSPARP PSPRLDVSSD SFDPLLALYA PRLPPIPYPN APCFNNVAEY ESFLRTGVRG GGRGRGRAR GAAAGSGVPA APGPSGRTRR RPDAPAPDPE RIQRLRRLMV AKEEGDGAAG AGRRGPGRSR KAPRNVLTRM P LHEGSPLG ELHRCIREGV KVNVHIRTFK GLRGVCTGFL VAFDKFWNMA LTDVDETYRK PVLQSRKKKR KPKVDYQQVF TR HINQIFI RGENVLLVHL AQ

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Macromolecule #8: Cleavage and polyadenylation specificity factor subunit 3

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.580883 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAIPAEESD QLLIRPLGAG QEVGRSCIIL EFKGRKIMLD CGIHPGLEGM DALPYIDLID PAEIDLLLIS HFHLDHCGAL PWFLQKTSF KGRTFMTHAT KAIYRWLLSD YVKVSNISAD DMLYTETDLE ESMDKIETIN FHEVKEVAGI KFWCYHAGHV L GAAMFMIE ...String:
MSAIPAEESD QLLIRPLGAG QEVGRSCIIL EFKGRKIMLD CGIHPGLEGM DALPYIDLID PAEIDLLLIS HFHLDHCGAL PWFLQKTSF KGRTFMTHAT KAIYRWLLSD YVKVSNISAD DMLYTETDLE ESMDKIETIN FHEVKEVAGI KFWCYHAGHV L GAAMFMIE IAGVKLLYTG DFSRQEDRHL MAAEIPNIKP DILIIESTYG THIHEKREER EARFCNTVHD IVNRGGRGLI PV FALGRAQ ELLLILDEYW QNHPELHDIP IYYASSLAKK CMAVYQTYVN AMNDKIRKQI NINNPFVFKH ISNLKSMDHF DDI GPSVVM ASPGMMQSGL SRELFESWCT DKRNGVIIAG YCVEGTLAKH IMSEPEEITT MSGQKLPLKM SVDYISFSAH TDYQ QTSEF IRALKPPHVI LVHGEQNEMA RLKAALIREY EDNDEVHIEV HNPRNTEAVT LNFRGEKLAK VMGFLADKKP EQGQR VSGI LVKRNFNYHI LSPCDLSNYT DLAMSTVKQT QAIPYTGPFN LLCYQLQKLT GDVEELEIQE KPALKVFKNI TVIQEP GMV VLEWLANPSN DMYADTVTTV ILEVQSNPKI RKGAVQKVSK KLEMHVYSKR LEIMLQDIFG EDCVSVKDDS ILSVTVD GK TANLNLETRT VECEEGSEDD ESLREMVELA AQRLYEALTP VH

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Macromolecule #9: Cleavage and polyadenylation specificity factor subunit 2

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 2
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.597734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTSIIKLTTL SGVQEESALC YLLQVDEFRF LLDCGWDEHF SMDIIDSLRK HVHQIDAVLL SHPDPLHLGA LPYAVGKLGL NCAIYATIP VYKMGQMFMY DLYQSRHNTE DFTLFTLDDV DAAFDKIQQL KFSQIVNLKG KGHGLSITPL PAGHMIGGTI W KIVKDGEE ...String:
MTSIIKLTTL SGVQEESALC YLLQVDEFRF LLDCGWDEHF SMDIIDSLRK HVHQIDAVLL SHPDPLHLGA LPYAVGKLGL NCAIYATIP VYKMGQMFMY DLYQSRHNTE DFTLFTLDDV DAAFDKIQQL KFSQIVNLKG KGHGLSITPL PAGHMIGGTI W KIVKDGEE EIVYAVDFNH KREIHLNGCS LEMLSRPSLL ITDSFNATYV QPRRKQRDEQ LLTNVLETLR GDGNVLIAVD TA GRVLELA QLLDQIWRTK DAGLGVYSLA LLNNVSYNVV EFSKSQVEWM SDKLMRCFED KRNNPFQFRH LSLCHGLSDL ARV PSPKVV LASQPDLECG FSRDLFIQWC QDPKNSIILT YRTTPGTLAR FLIDNPSEKI TEIELRKRVK LEGKELEEYL EKEK LKKEA AKKLEQSKEA DIDSSDESDI EEDIDQPSAH KTKHDLMMKG EGSRKGSFFK QAKKSYPMFP APEERIKWDE YGEII KPED FLVPELQATE EEKSKLESGL TNGDEPMDQD LSDVPTKCIS TTESIEIKAR VTYIDYEGRS DGDSIKKIIN QMKPRQ LII VHGPPEASQD LAECCRAFGG KDIKVYMPKL HETVDATSET HIYQVRLKDS LVSSLQFCKA KDAELAWIDG VLDMRVS KV DTGVILEEGE LKDDGEDSEM QVEAPSDSSV IAQQKAMKSL FGDDEKETGE ESEIIPTLEP LPPHEVPGHQ SVFMNEPR L SDFKQVLLRE GIQAEFVGGV LVCNNQVAVR RTETGRIGLE GCLCQDFYRI RDLLYEQYAI V

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Macromolecule #10: Symplekin

MacromoleculeName: Symplekin / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.355125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTTSERVVDL LNQAALITND SKITVLKQVQ ELIINKDPTL LDNFLDEIIA FQADKSIEVR KFVIGFIEEA CKRDIELLLK LIANLNMLL RDENVNVVKK AILTMTQLYK VALQWMVKSR VISELQEACW DMVSAMAGDI ILLLDSDNDG IRTHAIKFVE G LIVTLSPR ...String:
MTTSERVVDL LNQAALITND SKITVLKQVQ ELIINKDPTL LDNFLDEIIA FQADKSIEVR KFVIGFIEEA CKRDIELLLK LIANLNMLL RDENVNVVKK AILTMTQLYK VALQWMVKSR VISELQEACW DMVSAMAGDI ILLLDSDNDG IRTHAIKFVE G LIVTLSPR MADSEIPRRQ EHDISLDRIP RDHPYIQYNV LWEEGKAALE QLLKFMVHPA ISSINLTTAL GSLANIARQR PM FMSEVIQ AYETLHANLP PTLAKSQVSS VRKNLKLHLL SVLKHPASLE FQAQITTLLV DLGTPQAEIA RNMPSSKDTR KRP RDDSDS TLKKMKLEPN LGEDDEDKDL EPGPSGTSKA SAQISGQSDT DITAEFLQPL LTPDNVANLV LISMVYLPEA MPAS FQAIY TPVESAGTEA QIKHLARLMA TQMTAAGLGP GVEQTKQCKE EPKEEKVVKT ESVLIKRRLS AQGQAISVVG SLSSM SPLE EEAPQAKRRP EPIIPVTQPR LAGAGGRKKI FRLSDVLKPL TDAQVEAMKL GAVKRILRAE KAVACSGAAQ VRIKIL ASL VTQFNSGLKA EVLSFILEDV RARLDLAFAW LYQEYNAYLA AGASGSLDKY EDCLIRLLSG LQEKPDQKDG IFTKVVL EA PLITESALEV VRKYCEDESR TYLGMSTLRD LIFKRPSRQF QYLHVLLDLS SHEKDKVRSQ ALLFIKRMYE KEQLREYV E KFALNYLQLL VHPNPPSVLF GADKDTEVAA PWTEETVKQC LYLYLALLPQ NHKLIHELAA VYTEAIADIK RTVLRVIEQ PIRGMGMNSP ELLLLVENCP KGAETLVTRC LHSLTDKVPP SPELVKRVRD LYHKRLPDVR FLIPVLNGLE KKEVIQALPK LIKLNPIVV KEVFNRLLGT QHGEGNSALS PLNPGELLIA LHNIDSVKCD MKSIIKATNL CFAERNVYTS EVLAVVMQQL M EQSPLPML LMRTVIQSLT MYPRLGGFVM NILSRLIMKQ VWKYPKVWEG FIKCCQRTKP QSFQVILQLP PQQLGAVFDK CP ELREPLL AHVRSFTPHQ QAHIPNSIMT ILEAS

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Macromolecule #11: U7 snRNA

MacromoleculeName: U7 snRNA / type: rna / ID: 11 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.09718 KDa
SequenceString:
AGUGUUACAG CUCUUUUAGA AUUUGUCUAG UAGGCUUUCU GGCUUUUUAC CGGAAAGCCC

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Macromolecule #12: modified H2a pre-mRNA

MacromoleculeName: modified H2a pre-mRNA / type: rna / ID: 12 / Number of copies: 1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.626979 KDa
SequenceString:
CCAAAGGCUC UUUUCAGAGC CACCCACUGA AUCAGAUAAA GAGCUGUAAC AC

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5 / Component - Concentration: 100.0 mM / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 70.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 73.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 325282
Image recording ID1

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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